Locus 5242

Sequence ID X_DroMel_CAF1
Location 13,678,830 – 13,679,039
Length 209
Max. P 0.724442
window8491 window8492 window8493

overview

Window 1

Location 13,678,830 – 13,678,927
Length 97
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 76.30
Mean single sequence MFE -21.35
Consensus MFE -9.43
Energy contribution -14.67
Covariance contribution 5.25
Combinations/Pair 1.07
Mean z-score -2.52
Structure conservation index 0.44
SVM decision value 0.35
SVM RNA-class probability 0.700395
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13678830 97 + 22224390
CAUGACUGCCACUACGCCACUGUUUUCGUUAAUCAUUUGUAAUG-CAAAAUAAAUGCAAAAUGAGAACGGCGAAAAUUGGUUUCUUUUGAAACCAAUC
..............((((...(((((((((...(((((((....-....)))))))...)))))))))))))...(((((((((....))))))))). ( -28.30)
>DroSec_CAF1 10621 95 + 1
CAUGACUGC--CUACGCCACUGUUUUCGUUAAUCAUUUGUAAUG-CAAAAUAAAUGCAAAAUGAGAACGGCGAAAAUUGGUUUCUUUUGAAACCAAUC
.........--...((((...(((((((((...(((((((....-....)))))))...)))))))))))))...(((((((((....))))))))). ( -28.30)
>DroEre_CAF1 9621 73 + 1
-----------CUAGACCAAUCAUUUAGUCAAUCAUUUGCAAUG-CAGAAUAAACGC-------------CGAAAAUUGGUUUCUCUUAAUACCAAGC
-----------..((((((((..((..((......(((((...)-))))......))-------------..)).))))))))............... (  -9.60)
>DroYak_CAF1 10380 95 + 1
CAUGACCG---CUGCGCCACUGUUUUCGUUAAUCGUUUGUAAUGGCAAAAUAAAUGCAAAUUCAGAAUGGCGAAAAUUGGUUGCUUUUAAUACCAAUC
...(((((---.(.((((((((..((.((......(((((....)))))......)).))..)))..)))))...).)))))................ ( -19.20)
>consensus
CAUGACUG___CUACGCCACUGUUUUCGUUAAUCAUUUGUAAUG_CAAAAUAAAUGCAAAAUGAGAACGGCGAAAAUUGGUUUCUUUUAAAACCAAUC
..............((((...(((((((((...(((((((.........)))))))...)))))))))))))....((((((((....)))))))).. ( -9.43 = -14.67 +   5.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,678,848 – 13,678,964
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.59
Mean single sequence MFE -27.40
Consensus MFE -18.71
Energy contribution -19.93
Covariance contribution 1.23
Combinations/Pair 1.06
Mean z-score -2.29
Structure conservation index 0.68
SVM decision value 0.30
SVM RNA-class probability 0.680251
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13678848 116 + 22224390
ACUGUUUUCGUUAAUCAUUUGUAAUG-CAAAAUAAAUGCAAAAUGAGAACGGCGAAAAUUGGUUUCUUUUGAAACCAAUCAAAUUGUUUUG--GCUUCGCAAUAGU-GCAGUAUGCAAUU
.(((((((((((...(((((((....-....)))))))...))))))))))).....(((((((((....)))))))))..((((((....--(((.(((....))-).)))..)))))) ( -33.20)
>DroSec_CAF1 10637 109 + 1
ACUGUUUUCGUUAAUCAUUUGUAAUG-CAAAAUAAAUGCAAAAUGAGAACGGCGAAAAUUGGUUUCUUUUGAAACCAAUCAAAUUGUU-UG--GCUUCGCAAUAGU-GCAGUAU------
.(((((((((((...(((((((....-....)))))))...))))))))))).....(((((((((....))))))))).........-..--(((.(((....))-).)))..------ ( -29.10)
>DroYak_CAF1 10395 118 + 1
ACUGUUUUCGUUAAUCGUUUGUAAUGGCAAAAUAAAUGCAAAUUCAGAAUGGCGAAAAUUGGUUGCUUUUAAUACCAAUCGAAUUGUU-UAAUUCUACGCAAUAGCCACAGCAUGCAG-U
(((((....(((.....((((.....(((.......))).....)))).((((....((((((..........))))))...(((((.-((....)).))))).)))).)))..))))-) ( -19.90)
>consensus
ACUGUUUUCGUUAAUCAUUUGUAAUG_CAAAAUAAAUGCAAAAUGAGAACGGCGAAAAUUGGUUUCUUUUGAAACCAAUCAAAUUGUU_UG__GCUUCGCAAUAGU_GCAGUAUGCA__U
.(((((((((((...(((((((.........)))))))...))))))))))).....(((((((((....)))))))))...(((((...........)))))................. (-18.71 = -19.93 +   1.23)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,678,927 – 13,679,039
Length 112
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 68.86
Mean single sequence MFE -21.80
Consensus MFE -9.57
Energy contribution -9.83
Covariance contribution 0.25
Combinations/Pair 1.08
Mean z-score -2.05
Structure conservation index 0.44
SVM decision value 0.41
SVM RNA-class probability 0.724442
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13678927 112 - 22224390
UAUAUAUUGCCAACUCAUCUGCAUAUUUAUUGCAUUUUGUGUGCAAUUUAAUUUGUGGCAUGCAGUGUACAUUUAAAUUGCAUACUGC-ACUAUUGCGAAGC--CAAAACAAUUU
......((((........(..((.(((.(((((((.....)))))))..))).))..)..((((((((.((.......)).)))))))-).....))))...--........... ( -24.70)
>DroSec_CAF1 10716 92 - 1
UAUAUAUUGCCGACUCAUCUGCAUAUUUAUUGCACUUUUG-UGCAAUUUAAUUUGUGGAAUGC------------------AUACUGC-ACUAUUGCGAAGC--CA-AACAAUUU
......((((.......((..((.(((.(((((((....)-))))))..))).))..)).(((------------------.....))-).....))))...--..-........ ( -20.40)
>DroEre_CAF1 9694 87 - 1
U----AUUGCGACCUCAUCUGCAUAUUUAUUGCACUUUUG-UGCCAUUUAAUUUGCGGAAUUCGCUGUACAAUUGA-CUAC----UG-----------------UA-AACAAUUU
(----((.((((.....((((((.(((.((.((((....)-))).))..))).))))))..)))).))).......-....----..-----------------..-........ ( -18.00)
>DroYak_CAF1 10475 108 - 1
U----AUUGCAAACUCAUCUGCAUAUUUAUUGCACUUUUG-UGCAAUUUCAUUUGCGGAAUUCGAUGAACAUUUGA-CUGCAUGCUGUGGCUAUUGCGUAGAAUUA-AACAAUUC
.----.((((.......((((((.....(((((((....)-))))))......))))))..((((.......))))-..(((.((....))...))))))).....-........ ( -24.10)
>consensus
U____AUUGCCAACUCAUCUGCAUAUUUAUUGCACUUUUG_UGCAAUUUAAUUUGCGGAAUGCG_UGUACAUUUGA_CUGCAUACUGC_ACUAUUGCGAAGC__CA_AACAAUUU
.................((((((.....((((((.......))))))......))))))........................................................ ( -9.57 =  -9.83 +   0.25)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:05 2006